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# Packages

Search: "view:ExperimentData view:Preprocessing release:3.7"

The search reads these keywords as filters. Other words are searched as written.

- `license:MIT`: the licence family, by its name or an old keyword such as GPL
- `downloads:>1000`: at least that many distinct IPs a month
- `view:Bayesian`: a biocViews term, up to three
- `category:software`: a Bioconductor category: software, annotation, experiment or workflows
- `maintainer:"Hadley Wickham"`: the packages a person maintains now. Alone, with no catalogue in the address, their page
- `owner:tidyverse`: packages developed in that GitHub account's repositories. Alone, with no catalogue in the address, its page
- `ai:claude`: packages whose repository shows signs of that AI coding tool, ai:any of any tool
- `ai-found:pr`: how a tool was found: file, ignore, pr or commits
- `ai-model:opus`: a model named in the credit lines of commits
- `repo:yes`: a source repository on record, or repo:no
- `since:2026-01-01`: the latest release on or after that day
- `letter:D`: names that start with that letter
- `release:3.22`: the packages of a Bioconductor release, or release:all for every package ever seen
- `status:removed`: Bioconductor packages removed after an earlier release, status:unreleased never in one
- `-checks:failing`: a minus before checks, license, view, maintainer, owner, ai, ai-model, letter, tests or category leaves those packages out, and before compiled, deadline or repo gives the other answer
- `in:bioc`: a catalogue: all, cran, bioc, archived, or datasets for Datasets' search
- `sort:downloads`: an order: name, downloads, updated, or relevance for words alone

Catalogue: Bioconductor.
- Bioconductor release: Release 3.7 (2018)
- biocViews term: ExperimentData
- biocViews term: Preprocessing
- Topic page: [ExperimentData](/topics/bioc/ExperimentData.md)
- Topic page: [Preprocessing](/topics/bioc/Preprocessing.md)

528 packages on Bioconductor tagged ExperimentData or Preprocessing, most distinct IPs first.

To search, add ?q=WORDS. To pick a catalogue, add catalogue=all, catalogue=cran or catalogue=bioc. To order the list, add sort=name, category, published, downloads, dependencies and order=asc or order=desc. Filters for Bioconductor: status (In the current release or not), release (Bioconductor release), category (Category), view (biocViews term), min_downloads (Distinct IPs a month), letter (First letter), license (Licence family offered), repository (Source repository on GitHub known), published_since (Latest version published on or after), maintainer (Maintainer), owner (Repository owner on GitHub), ai (AI coding tool), ai_found (AI tool found as), ai_model (Model named in commits). view takes up to three terms joined by commas, and lists packages tagged with any of them. min_downloads takes any whole number. maintainer takes a person's whole name and owner a GitHub login. ai takes any or a tool's key, ai_found file, ignore, pr or commits, and ai_model a model family's key, with the values and counts the page offers. not_ before the name of letter, license, check, task_view, tests, maintainer, owner, ai, ai_model, category or view leaves those packages out, as in not_check=problems.

| Package | Maintainer | Category | Latest version | Distinct IPs a month (sorted, high to low) | Needs |
| --- | --- | --- | --- | ---: | ---: |
| [limma](/bioc/limma.md) Linear Models for Microarray and Omics Data | Gordon Smyth | software | 10 Aug 2026 | 45,965 | 6 |
| [ggtree](/bioc/ggtree.md) an R package for visualization of tree and annotation data | Guangchuang Yu | software | 29 Oct 2026 | 34,372 | 79 |
| [scater](/bioc/scater.md) Single-Cell Analysis Toolkit for Gene Expression Data in R | Alan O'Callaghan | software | 2 Jul 2026 | 12,635 | 78 |
| [sva](/bioc/sva.md) Surrogate Variable Analysis | Jeffrey T. Leek | software | 5 May 2026 | 10,804 | 68 |
| [affy](/bioc/affy.md) Methods for Affymetrix Oligonucleotide Arrays | Robert D. Shear | software | 28 Apr 2026 | 10,556 | 11 |
| [vsn](/bioc/vsn.md) Variance stabilization and calibration for microarray data | Wolfgang Huber | software | 28 Apr 2026 | 7,536 | 33 |
| [biovizBase](/bioc/biovizBase.md) Basic graphic utilities for visualization of genomic data. | Michael Lawrence | software | 28 Apr 2026 | 6,487 | 126 |
| [tximport](/bioc/tximport.md) Import and summarize transcript-level estimates for transcript- and gene-level analysis | Michael Love | software | 28 Apr 2026 | 5,804 | 3 |
| [TCGAbiolinksGUI.data](/bioc/TCGAbiolinksGUI.data.md) Data for the TCGAbiolinksGUI package | Tiago Chedraoui Silva | experiment | 5 May 2026 | 5,758 | 0 |
| [ALL](/bioc/ALL.md) A data package | Robert Gentleman | experiment | 5 May 2026 | 4,171 | 7 |
| [oligo](/bioc/oligo.md) Preprocessing tools for oligonucleotide arrays | Benilton Carvalho | software | 28 Apr 2026 | 4,087 | 52 |
| [minfi](/bioc/minfi.md) Analyze Illumina Infinium DNA methylation arrays | Kasper Daniel Hansen | software | 28 Apr 2026 | 4,041 | 143 |
| [cytolib](/bioc/cytolib.md) C++ infrastructure for representing and interacting with the gated cytometry data | Mike Jiang | software | 28 Apr 2026 | 3,820 | 8 |
| [HSMMSingleCell](/bioc/HSMMSingleCell.md) Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM) | Cole Trapnell | experiment | 5 May 2026 | 3,553 | 0 |
| [marray](/bioc/marray.md) Exploratory analysis for two-color spotted microarray data | Yee Hwa (Jean) Yang | software | 28 Apr 2026 | 3,311 | 7 |
| [variancePartition](/bioc/variancePartition.md) Quantify and interpret drivers of variation in multilevel gene expression experiments | Gabriel E. Hoffman | software | 28 Apr 2026 | 3,211 | 99 |
| [Rsubread](/bioc/Rsubread.md) Mapping, quantification and variant analysis of sequencing data | Wei Shi | software | 28 Apr 2026 | 2,951 | 8 |
| [airway](/bioc/airway.md) RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014 | Michael Love | experiment | 5 May 2026 | 2,854 | 25 |
| [methylumi](/bioc/methylumi.md) Handle Illumina methylation data | Sean Davis | software | 16 Aug 2026 | 2,825 | 158 |
| [flowWorkspace](/bioc/flowWorkspace.md) Infrastructure for representing and interacting with gated and ungated cytometry data sets. | Greg Finak | software | 28 Apr 2026 | 2,804 | 61 |
| [EDASeq](/bioc/EDASeq.md) Exploratory Data Analysis and Normalization for RNA-Seq | Davide Risso | software | 28 Apr 2026 | 2,602 | 111 |
| [aroma.light](/bioc/aroma.light.md) Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types | Henrik Bengtsson | software | 28 Apr 2026 | 2,481 | 8 |
| [lumi](/bioc/lumi.md) BeadArray Specific Methods for Illumina Methylation and Expression Microarrays | Lei Huang | software | 28 Apr 2026 | 2,454 | 165 |
| [affyPLM](/bioc/affyPLM.md) Methods for fitting probe-level models | Ben Bolstad | software | 28 Apr 2026 | 2,430 | 22 |
| [geneLenDataBase](/bioc/geneLenDataBase.md) Lengths of mRNA transcripts for a number of genomes | Federico Marini | experiment | 5 May 2026 | 2,378 | 98 |
| [Mfuzz](/bioc/Mfuzz.md) Soft clustering of omics time series data | Matthias Futschik | software | 28 Apr 2026 | 2,353 | 16 |
| [scRNAseq](/bioc/scRNAseq.md) Collection of Public Single-Cell RNA-Seq Datasets | Aaron Lun | experiment | 5 May 2026 | 2,314 | 121 |
| [gcrma](/bioc/gcrma.md) Background Adjustment Using Sequence Information | Z. Wu | software | 28 Apr 2026 | 2,285 | 21 |
| [bcellViper](/bioc/bcellViper.md) Human B-cell transcriptional interactome and normal human B-cell expression data | Mariano Javier Alvarez | experiment | 5 May 2026 | 2,177 | 7 |
| [openCyto](/bioc/openCyto.md) Hierarchical Gating Pipeline for flow cytometry data | Mike Jiang | software | 28 Apr 2026 | 2,028 | 75 |

This page lists 1 to 30 of 528 packages. [Next](/packages.md?catalogue=bioc&release=3.7&view=ExperimentData%2CPreprocessing&sort=downloads&page=2)

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